[Chimera-users] Using sym command to generate icosahedral cage

Tom Goddard goddard at sonic.net
Mon Feb 24 18:10:54 PST 2014

Hi Yen,

There is no simple way to specify a coordinate frame in Chimera using vectors (although it is easy in Python).  For symmetries with a single symmetry axis like cyclic symmetry you can specify the "axis" keyword and a vector (3 comma-separated numbers) to the sym command and it will use that as the symmetry axis.  This will work for icosahedral symmetry but only allows you to reorient the z axis of one of the standard orientations.  The coordinateSystem option to the sym command lets you use the axes of another model for the symmetry.  But there is no Chimera command to specify the coordinate axes of one model as vectors relative to the coordinate system of another model.

You are asking for something pretty exotic.  If you explain more about your problem (how you get this coordinate system as vectors) maybe I'll have and idea for how to make the symmetry work.  For instance the Chimera matrixget can read vector coordinate frames from a file and maybe that could be used in your situation.


On Feb 21, 2014, at 4:49 PM, Yen-Ting Lai wrote:

> Hi,
> I noticed that the sym command can be used to generate icosahedral symmetry, but it requires that the molecule to be oriented in specific ways (222, 2n5, n25, ...), which requires aligning the symmetry axes to the X, Y or Z axes. I am wondering if there is a way to specify the symmetries axes by vectors (instead of aligning them to the three principal axes) and then use sym command to generate the whole icosahedral cage?
> Yen
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